01. Prepare grey and white maps for DARTEL

This step enables to manage input DARTEL data as required in SPM, i.e. all inputs have to be in a common space (here Talairach), with a common 'internal referential' in the headers, and be resampled within a same isotropic resolution and volume dimensions. In comparison with the standard procedure, the DARTEL inputs will be binary segmentations (grey and white) and not probabilistic maps.

Data to be aligned may directly come from Morphologist (Native mode), or previously aligned with Disco pipeline (AfterDISCO mode). Note that even in Native mode, a study directory and a subjects_hierarchy file defined in the first steps of DISCO, are required.

1. Choose the type of the study (Native or AfterDISCO).

2. Select the study directory of the experiment.

3. Add a translation to enable the volumes resampling in Talairach referential (exple in /neurospin/hbp/Users/jlebenberg/AC_translation.trm.

4. Note resolution, dimensions and crop parameters as they are required in 03. DARTEL Images Warping, 04. DARTEL Images Inverse Warping, Create DISCO+DARTEL deformation field toward the common space and Create DISCO+DARTEL deformation field from subjectA to subjectB.

5. Save the crop transformation in crop_dir_trm and crop_inv_trm parameters as they are required in 04. DARTEL Images Inverse Warping, Create DISCO+DARTEL deformation field toward the common space and Create DISCO+DARTEL deformation field from subjectA to subjectB.

Both step are described in DARTEL components.

Parameters

study_type: Choice ( input )

Type of the study (Native or AfterDISCO)

study_dir: DISCO Study Dir ( input )

Study directory of the experiment

subjects_hierarchy: Save Subjects Hierarchy DISCO ( input )

Lgrey_white_DISCO: ListOf( Grey White Mask Corrected DISCO ) ( input )

Rgrey_white_DISCO: ListOf( Grey White Mask Corrected DISCO ) ( input )

Talairach_transforms: ListOf( Transform Graph to Talairach-AC/PC-Anatomist ) ( input )

resample_in_Talairach: Boolean ( input )

if True, DARTEL input grey-white maps will be resampled in Talairach space.

boundingbox_min_mm: ListOf( Float ) ( input )

boundingbox_max_mm: ListOf( Float ) ( input )

isotropic_resolution_mm: Float ( input )

compo_To_Tal: ListOf( Compo To Resample To Talairach ) ( optional, output )

Composition of volume_Talairach_resample and crop_dir_trm

dartel_space_TO_Talairach: Transform DARTEL Input Space to Talairach-AC/PC-Anatomist ( output )

Grey_DISCO: ListOf( Grey Mask Corrected DISCO ) ( output )

White_DISCO: ListOf( White Mask Corrected DISCO ) ( output )

Technical information

Toolbox : Disco

User level : 0

Identifier : DartelPreProcess

File name : brainvisa/toolboxes/disco/processes/DARTEL_components/DartelPreProcess.py

Supported file formats :

study_dir :

Directory, Directory

subjects_hierarchy :

Text file, Text file

Lgrey_white_DISCO :

NIFTI-1 image, NIFTI-1 image

Rgrey_white_DISCO :

NIFTI-1 image, NIFTI-1 image

Talairach_transforms :

Transformation matrix, Transformation matrix

compo_To_Tal :

Transformation matrix, Transformation matrix

dartel_space_TO_Talairach :

Transformation matrix, Transformation matrix

Grey_DISCO :

NIFTI-1 image, NIFTI-1 image

White_DISCO :

NIFTI-1 image, NIFTI-1 image